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Keywords: QC 

ChIP-seq analysis using R - Quality Control

This practical illustrates steps that can be undertaken to assess the quality of the sequencing data. We will start from the fastq files and assess their quality in respect to potential contamination and technical artifacts.

Scientific topics: RNA-Seq

Keywords: ChIP-Seq, RNA-Seq, QC, Data-format, Experimental-design

ChIP-seq analysis using R - Quality Control https://tess.elixir-europe.org/materials/chip-seq-analysis-using-r-quality-control This practical illustrates steps that can be undertaken to assess the quality of the sequencing data. We will start from the fastq files and assess their quality in respect to potential contamination and technical artifacts. RNA-Seq ChIP-Seq, RNA-Seq, QC, Data-format, Experimental-design
ChIP-seq analysis using R - File formats and QC

This lecture introduces the file formats of sequencing data before alignment and covers the general quality control of sequencing data focussing on RNA-Seq and ChIP-Seq.

Scientific topics: RNA-Seq

Keywords: ChIP-Seq, RNA-Seq, QC, Data-format, Experimental-design

ChIP-seq analysis using R - File formats and QC https://tess.elixir-europe.org/materials/chip-seq-analysis-using-r-file-formats-and-qc This lecture introduces the file formats of sequencing data before alignment and covers the general quality control of sequencing data focussing on RNA-Seq and ChIP-Seq. RNA-Seq ChIP-Seq, RNA-Seq, QC, Data-format, Experimental-design
ChIP-seq analysis using R - Mapping and file formats

This lecture introduces the principles behind alignment, different tools and de-novo assembly. It also covers post mapping data format and quality control

Scientific topics: Sequence assembly, RNA-Seq

Keywords: ChIP-Seq, RNA-Seq, Alignment, Data-format, Assembly, QC

ChIP-seq analysis using R - Mapping and file formats https://tess.elixir-europe.org/materials/chip-seq-analysis-using-r-mapping-and-file-formats This lecture introduces the principles behind alignment, different tools and de-novo assembly. It also covers post mapping data format and quality control Sequence assembly RNA-Seq ChIP-Seq, RNA-Seq, Alignment, Data-format, Assembly, QC
ChIP-seq analysis using R - Quality Control Walkthrough

This practical illustrates steps that can be undertaken to assess the quality of the sequencing data. We will start from the fastq files and assess their quality in respect to potential contamination and technical artifacts.

Scientific topics: RNA-Seq

Keywords: ChIP-Seq, RNA-Seq, QC, Data-format, Experimental-design

ChIP-seq analysis using R - Quality Control Walkthrough https://tess.elixir-europe.org/materials/chip-seq-analysis-using-r-quality-control-walkthrough This practical illustrates steps that can be undertaken to assess the quality of the sequencing data. We will start from the fastq files and assess their quality in respect to potential contamination and technical artifacts. RNA-Seq ChIP-Seq, RNA-Seq, QC, Data-format, Experimental-design
Variant-calling

No description available

Keywords: Alignment, Annotation, BAM, BCF, De-novo-transcriptome-assembly, Exploratory-analysis, FASTQ, Pre-processing, QC, Statistical-model, Variant-calling, VCF

Variant-calling https://tess.elixir-europe.org/materials/variant-calling No description available Alignment, Annotation, BAM, BCF, De-novo-transcriptome-assembly, Exploratory-analysis, FASTQ, Pre-processing, QC, Statistical-model, Variant-calling, VCF
Introduction to RNA-seq analysis 2014

This lecture gives an overview how to perform an RNA-seq experiment. A general RNA-seq workflow is outlined when a good quality genome sequence is available for your species.

Keywords: Alignment, Differential-expression, Feature-summarisation, Pre-processing, QC

Introduction to RNA-seq analysis 2014 https://tess.elixir-europe.org/materials/introduction-to-rna-seq-analysis-2014 This lecture gives an overview how to perform an RNA-seq experiment. A general RNA-seq workflow is outlined when a good quality genome sequence is available for your species. Alignment, Differential-expression, Feature-summarisation, Pre-processing, QC
RNA-seq training PSB 2013

This lecture gives an overview how to perform an RNA-seq experiment. First, the Illumina sequencing platform is briefly covered, followed by the different file formats in NGS. Next, an RNA-seq workflow is outlined, starting from the raw data up to differential expression. The recommended coverage...

Keywords: Alignment, Differential-expression, Feature-summarisation, Pre-processing, QC

RNA-seq training PSB 2013 https://tess.elixir-europe.org/materials/rna-seq-training-psb-2013 This lecture gives an overview how to perform an RNA-seq experiment. First, the Illumina sequencing platform is briefly covered, followed by the different file formats in NGS. Next, an RNA-seq workflow is outlined, starting from the raw data up to differential expression. The recommended coverage and sequencing mode is touched upon as well as the effect on your analysis of divergence of your genotype compared to the reference. Alignment, Differential-expression, Feature-summarisation, Pre-processing, QC
Material for the course RNA-seq data analysis with Chipster

This material covers the whole RNA-seq data analysis pipeline, from quality control of raw reads to differential expression analysis.

Scientific topics: RNA-Seq

Keywords: RNA-Seq, FASTQ, QC, Pre-processing, Alignment, BAM, Expression-estimation, Feature-summarisation, Differential-expression, Statistical-model, Exploratory-analysis

Material for the course RNA-seq data analysis with Chipster https://tess.elixir-europe.org/materials/material-for-the-course-rna-seq-data-analysis-with-chipster This material covers the whole RNA-seq data analysis pipeline, from quality control of raw reads to differential expression analysis. RNA-Seq RNA-Seq, FASTQ, QC, Pre-processing, Alignment, BAM, Expression-estimation, Feature-summarisation, Differential-expression, Statistical-model, Exploratory-analysis
RNA-seq module Bert Overduin

All material concerning RNA-seq analysis

Scientific topics: RNA-Seq

Keywords: RNA-Seq, Pre-processing, QC, Alignment

RNA-seq module Bert Overduin https://tess.elixir-europe.org/materials/rna-seq-module-bert-overduin All material concerning RNA-seq analysis RNA-Seq RNA-Seq, Pre-processing, QC, Alignment
Nicolas Delhomme and Bastian Schiffthaler

This merely lists the various courses at which we taught RNA-Seq data

Scientific topics: RNA-Seq

Keywords: FASTQ, GFF3, BAM, Populus-tremula, RNA-Seq, Pre-processing, QC, Alignment, Annotation, Expression-estimation, Differential-expression, R-programming

Nicolas Delhomme and Bastian Schiffthaler https://tess.elixir-europe.org/materials/nicolas-delhomme-and-bastian-schiffthaler This merely lists the various courses at which we taught RNA-Seq data RNA-Seq FASTQ, GFF3, BAM, Populus-tremula, RNA-Seq, Pre-processing, QC, Alignment, Annotation, Expression-estimation, Differential-expression, R-programming
Mapping Quality Control

Perform QC on aligned data

Keywords: Alignment, BAM, QC

Mapping Quality Control https://tess.elixir-europe.org/materials/mapping-quality-control Perform QC on aligned data Alignment, BAM, QC
Day 3 - RNA-Seq Analysis

Day 3 focuses on statistical analysis of RNA-Seq data and identification of differentiall expressed genes in multiple comparisons.

Keywords: QC, Exploratory-analysis, Differential-expression, Statistical-model, Pre-processing

Day 3 - RNA-Seq Analysis https://tess.elixir-europe.org/materials/day-3-rna-seq-analysis Day 3 focuses on statistical analysis of RNA-Seq data and identification of differentiall expressed genes in multiple comparisons. QC, Exploratory-analysis, Differential-expression, Statistical-model, Pre-processing
ChIP-Seq

No description available

Keywords: ChIP-Seq, Experimental-design, QC, ChIP-Seq-QC, Data-format, Alignment, Peak-calling, Differential-binding, Annotation

ChIP-Seq https://tess.elixir-europe.org/materials/chip-seq No description available ChIP-Seq, Experimental-design, QC, ChIP-Seq-QC, Data-format, Alignment, Peak-calling, Differential-binding, Annotation
Tutorial

This file describes the main tutorial PDF file. Almost all tutorials and hands-on practices are indeed collated in a single document. In addition to this PDF, R code excerpts and installation instructions are also provided.

Scientific topics: RNA-Seq

Keywords: FASTQ, GFF3, BAM, Populus-tremula, RNA-Seq, Pre-processing, QC, Alignment, Annotation, Expression-estimation, R-programming

Tutorial https://tess.elixir-europe.org/materials/tutorial This file describes the main tutorial PDF file. Almost all tutorials and hands-on practices are indeed collated in a single document. In addition to this PDF, R code excerpts and installation instructions are also provided. RNA-Seq FASTQ, GFF3, BAM, Populus-tremula, RNA-Seq, Pre-processing, QC, Alignment, Annotation, Expression-estimation, R-programming
RNA-Seq Analysis with Biocluster and R

Sequencing of RNA (RNA-Seq) is the latest method to assess global gene expression because it

Scientific topics: RNA-Seq

Keywords: RNA-Seq, Alignment, Annotation, BAM, Differential-expression, Exploratory-analysis, Expression-estimation, FASTA, FASTQ, Feature-summarisation, Pre-processing, QC, Statistical-model

RNA-Seq Analysis with Biocluster and R https://tess.elixir-europe.org/materials/rna-seq-analysis-with-biocluster-and-r Sequencing of RNA (RNA-Seq) is the latest method to assess global gene expression because it RNA-Seq RNA-Seq, Alignment, Annotation, BAM, Differential-expression, Exploratory-analysis, Expression-estimation, FASTA, FASTQ, Feature-summarisation, Pre-processing, QC, Statistical-model
RNA-seq module Eija Korpelainen

All material concerning RNA-seq data analysis with Chipster

Keywords: FASTQ, QC, Pre-processing, Alignment, BAM, Expression-estimation, Feature-summarisation, Differential-expression, Statistical-model, Exploratory-analysis

RNA-seq module Eija Korpelainen https://tess.elixir-europe.org/materials/rna-seq-module-eija-korpelainen All material concerning RNA-seq data analysis with Chipster FASTQ, QC, Pre-processing, Alignment, BAM, Expression-estimation, Feature-summarisation, Differential-expression, Statistical-model, Exploratory-analysis
Populus tremula shows no evidence of sexual dimorphism

**Background:** Although the majority of plant species are co-sexual, being either monoecious or hermaphroditic, a significant number are dioecious, having separate male and female individuals. Evolutionary theory suggests that males and females may develop sexually dimorphic phenotypic and...

Scientific topics: RNA-Seq

Keywords: FASTQ, GFF3, BAM, Populus-tremula, RNA-Seq, Pre-processing, QC, Alignment, Annotation, Expression-estimation, Differential-expression

Populus tremula shows no evidence of sexual dimorphism https://tess.elixir-europe.org/materials/populus-tremula-shows-no-evidence-of-sexual-dimorphism **Background:** Although the majority of plant species are co-sexual, being either monoecious or hermaphroditic, a significant number are dioecious, having separate male and female individuals. Evolutionary theory suggests that males and females may develop sexually dimorphic phenotypic and biochemical traits concordant with each sex having different optimal strategies of resource investment to maximise reproductive success and fitness. The establishment of such sexual dimorphism would result in changes in gene expression patterns in non-floral organs. RNA-Seq FASTQ, GFF3, BAM, Populus-tremula, RNA-Seq, Pre-processing, QC, Alignment, Annotation, Expression-estimation, Differential-expression
Nicolas Delhomme - Bastian Schiffthaler - October 2014 EMBO course material

Material for the course held on EBI Campus, Welcome Trust Center, Hinxton, UK on 20-26th, October 2014. The material cover general RNA-Seq data pre-processing as described in these [guidelines](http://www.epigenesys.eu/en/protocols/bio-informatics/1283-guidelines-for-rna-seq-data-analysis) and...

Scientific topics: RNA-Seq

Keywords: FASTQ, GFF3, BAM, Populus-tremula, RNA-Seq, Pre-processing, QC, Alignment, Annotation, Expression-estimation, Differential-expression, R-programming

Nicolas Delhomme - Bastian Schiffthaler - October 2014 EMBO course material https://tess.elixir-europe.org/materials/nicolas-delhomme-bastian-schiffthaler-october-2014-embo-course-material Material for the course held on EBI Campus, Welcome Trust Center, Hinxton, UK on 20-26th, October 2014. The material cover general RNA-Seq data pre-processing as described in these [guidelines](http://www.epigenesys.eu/en/protocols/bio-informatics/1283-guidelines-for-rna-seq-data-analysis) and reproduces the Differential Expression analysis conducted in Robinson, Delhomme et al., 2014. RNA-Seq FASTQ, GFF3, BAM, Populus-tremula, RNA-Seq, Pre-processing, QC, Alignment, Annotation, Expression-estimation, Differential-expression, R-programming
Exercises for the course RNA-seq data analysis with Chipster

This practical covers the whole RNA-seq data analysis pipeline, from quality control of raw reads to differential expression analysis, using the free Chipster software. Material updated in Dec 2015.

Keywords: FASTQ, QC, Pre-processing, Alignment, BAM, Expression-estimation, Feature-summarisation, Differential-expression, Statistical-model, Exploratory-analysis

Exercises for the course RNA-seq data analysis with Chipster https://tess.elixir-europe.org/materials/exercises-for-the-course-rna-seq-data-analysis-with-chipster This practical covers the whole RNA-seq data analysis pipeline, from quality control of raw reads to differential expression analysis, using the free Chipster software. Material updated in Dec 2015. FASTQ, QC, Pre-processing, Alignment, BAM, Expression-estimation, Feature-summarisation, Differential-expression, Statistical-model, Exploratory-analysis
Day 1 - RNA-Seq Analysis

Day 1 starts at the very beginning of a typical RNA-Seq workflow, explaining the sequencing technology and considerations for experimental design, then starts with hands-on application of working with sequencing data fresh off the sequencer.

Keywords: Alignment, BAM, FASTA, FASTQ, QC

Day 1 - RNA-Seq Analysis https://tess.elixir-europe.org/materials/day-1-rna-seq-analysis Day 1 starts at the very beginning of a typical RNA-Seq workflow, explaining the sequencing technology and considerations for experimental design, then starts with hands-on application of working with sequencing data fresh off the sequencer. Alignment, BAM, FASTA, FASTQ, QC
Introduction to NGS and RNA-seq

No description available

Keywords: HTS-introduction, Data-format, Alignment, Differential-expression, Feature-summarisation, QC

Introduction to NGS and RNA-seq https://tess.elixir-europe.org/materials/introduction-to-ngs-and-rna-seq No description available HTS-introduction, Data-format, Alignment, Differential-expression, Feature-summarisation, QC
RNA-seq module Frederik Coppens

All material concerning RNA-seq analysis

Scientific topics: RNA-Seq

Keywords: RNA-Seq, Alignment, BAM, FASTQ, Feature-summarisation, Pre-processing, QC

RNA-seq module Frederik Coppens https://tess.elixir-europe.org/materials/rna-seq-module-frederik-coppens All material concerning RNA-seq analysis RNA-Seq RNA-Seq, Alignment, BAM, FASTQ, Feature-summarisation, Pre-processing, QC
Day 2 - RNA-Seq Analysis

Day 2 continues throught the steps in a typical RNA-Seq experiment from alignment to sample QC and count normalization, including a brief overview of the IGV Genome Browser.

Keywords: Alignment, BAM, FASTA, FASTQ, QC, Exploratory-analysis, Feature-summarisation, Pre-processing

Day 2 - RNA-Seq Analysis https://tess.elixir-europe.org/materials/day-2-rna-seq-analysis Day 2 continues throught the steps in a typical RNA-Seq experiment from alignment to sample QC and count normalization, including a brief overview of the IGV Genome Browser. Alignment, BAM, FASTA, FASTQ, QC, Exploratory-analysis, Feature-summarisation, Pre-processing
ChIP-seq analysis using R

ChIP-seq is the most commonly used technique to study binding profiles of chromatin proteins, such as TFs or histone modification patterns. This course is an introduction to ChIP-seq data, and data analysis mainly using R, some command line based peak-callers and online software. It provides a...

Keywords: ChIP-Seq, Experimental-design, QC, Data-format, Alignment, Peak-calling, Differential-binding, Visualisation, Annotation

ChIP-seq analysis using R https://tess.elixir-europe.org/materials/chip-seq-analysis-using-r ChIP-seq is the most commonly used technique to study binding profiles of chromatin proteins, such as TFs or histone modification patterns. This course is an introduction to ChIP-seq data, and data analysis mainly using R, some command line based peak-callers and online software. It provides a theoretical background and the means to perform peak calling and differential binding analysis. ChIP-Seq, Experimental-design, QC, Data-format, Alignment, Peak-calling, Differential-binding, Visualisation, Annotation
Alignment

Introduction to short-read alignments, including a general overview of existing methods (Burrow-Wheeler-Transform, Maximum Mappable Prefix, _etc._) and some cautionary tales.

Scientific topics: RNA-Seq

Keywords: BAM, Populus-tremula, RNA-Seq, QC, Alignment

Alignment https://tess.elixir-europe.org/materials/alignment Introduction to short-read alignments, including a general overview of existing methods (Burrow-Wheeler-Transform, Maximum Mappable Prefix, _etc._) and some cautionary tales. RNA-Seq BAM, Populus-tremula, RNA-Seq, QC, Alignment
Lecture slides for the course RNA-seq data analysis with Chipster

This material covers the whole RNA-seq data analysis pipeline, from quality control of raw reads to differential expression analysis. It discusses also experimental design. Material updated in Dec 2015.

Keywords: FASTQ, QC, Pre-processing, Alignment, BAM, Expression-estimation, Feature-summarisation, Differential-expression, Statistical-model, Exploratory-analysis

Lecture slides for the course RNA-seq data analysis with Chipster https://tess.elixir-europe.org/materials/lecture-slides-for-the-course-rna-seq-data-analysis-with-chipster This material covers the whole RNA-seq data analysis pipeline, from quality control of raw reads to differential expression analysis. It discusses also experimental design. Material updated in Dec 2015. FASTQ, QC, Pre-processing, Alignment, BAM, Expression-estimation, Feature-summarisation, Differential-expression, Statistical-model, Exploratory-analysis
EMBO High Throughput Sequencing Data Analysis, Cambridge, UK, 2014

No description available

Scientific topics: RNA-Seq

Keywords: FASTQ, GFF3, BAM, Populus-tremula, RNA-Seq, Pre-processing, QC, Alignment, Annotation, Expression-estimation, Differential-expression, R-programming

EMBO High Throughput Sequencing Data Analysis, Cambridge, UK, 2014 https://tess.elixir-europe.org/materials/embo-high-throughput-sequencing-data-analysis-cambridge-uk-2014 No description available RNA-Seq FASTQ, GFF3, BAM, Populus-tremula, RNA-Seq, Pre-processing, QC, Alignment, Annotation, Expression-estimation, Differential-expression, R-programming
Quality Control

This is an introduction to the tools available for performing the technical QA of RNA-Seq data and to their results, singling out possible common caveats.

Scientific topics: RNA-Seq

Keywords: FASTQ, RNA-Seq, Pre-processing, QC

Quality Control https://tess.elixir-europe.org/materials/quality-control This is an introduction to the tools available for performing the technical QA of RNA-Seq data and to their results, singling out possible common caveats. RNA-Seq FASTQ, RNA-Seq, Pre-processing, QC